Version 1.4.1

Changes:

• Uses pyproject.toml instead of setup.py for installation
• update minimal requirement for ncbi_genome_download to be compatible with the last NCBI format (issue #42)
• use --amino option for mafft protein alignements in order to force sequence type to be proteic and deal with ambiguous aa (see 728445d#commitcomment-122306169)
• fix issue with protein names. They must fulfill the conditions described in https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#protein-files

Version 1.4.0

Changes:

General

• Use of number of CPUs available to the process instead of the total number of CPUs on the machine (issue #37). (NB: Mac OS users will still be using the total number of CPUs)
• Update conda recipe to be compatible with python > 3.6 (issue #38)

prepare:

• new option to download a single strain (issue #17)

tree:

• new option: write distance matrix when using fastME (issue #36)

Version 1.3.1

Fix issue #16 : bootstrapping from "PanACoTA all" module via configfile is now working

Version 1.3.0

Changes:

all:
fixes issue #11 (cutN not taken into account when launched from configfile)

pangenome:

• Fixes issue #14
• changes in output directory structure (all mmseqs files in a separate directory, and simpler default pangenome filename)

corepers:
possibility to give a subset of genomes for the coregenome (instead of all genomes found in pan)

align:

• Add possibility to ask for proteic alignments concatenated by genomes (in addition to nucleic ones)
• fix logger detail issue
• genome names can now contain a '.'

tree:

• add TEST parameter when using IQtree
• fix problem if user has iqtree2 version called by iqtree command.

Version 1.2.0

Changes:

Module 'all'

• configuration file for 'all' module: when running 'all' subcommand, it is now possible to choose all parameters for all modules, using a configuration file.

Module prepare

• 0 included when we ask for a mash min_dist = 0
• add choice for NCBI section: genbank or refseq
• add possibility to give a ncbi taxid (-t, for a subspecies or a specific strain) in addition to ncbi species taxid (-T)

Module annotate

• prodigal now uses training mode on the first genome (the one with best quality) before annotating all genomes
• fix bug logger has no attribute detail

Version 1.1.0

Changes:

• Major change: new module to run everything in a row: 'all' module. See PanACoTA all -h
• Fix bug when there is a binary file in the genomes repository
• IQtree2 is the default software when running PanACoTA tree. To use IQtree versions 1.x, use -s iqtree option

Version 1.0.1

CHANGES:

• fix problems while formatting genomes annotated by prokka
• add new option, to select the assembly level of genomes to download from NCBI

First release

v1.0

version 1.0